In 1864, Muir took a train from Madison, Wisconsin via Chicago on March 1, 1864 he crossed the international border at Windsor, Canada West, which later became the Province of Ontario, Canada.
In summer 1867, after recovering his eyesight, Muir walked across Indiana and Illinois on a botanizing excursion, with his final destination Madison and the old homestead at Fountain Lake. His companion was eleven-year-old Merrill Moores, of the extended family of Catherine Merrill, who had nursed him during his convalescence from his eye injury. Avoiding the railroads, they walked across prairies not yet ploughed, covered with flowers, fossils and minerals. They hiked along the banks of the Vermillion River, passed through Bloomington, Illinois, and on north to Rockford, Illinois, where they caught a train to Wisconsin.
Chicago: In August of 1867, Muir reported to his friend Jeanne Carr regarding a brief stop he had in Chicago that month: "I could not but notice how well appearances in the vicinity of Chicago agreed with Lesquereux's theory of the formation of prairies. We spent about five hours in Chicago. I did not find many flowers in her tumultuous streets; only a few grassy plants of wheat and two or three species of weeds,--amaranth, purslane, carpet-weed, etc.,--the weeds, I suppose, for man to walk upon, the wheat to feed him. I saw some new alga, but no mosses. I expected to see some of the latter on wet walls and in seams in the pavement, but I suppose that the manufacturers' smoke and the terrible noise is too great for the hardiest of them."
In May of 1893, Muir visited the Chicago World's Fair; finding it "a cosmopolitan rat's nest." (In Wolfe, Son of the Wilderness). In a letter to his wife Louie, he expanded on his assessment: "I ...have seen the best of it though months would be required to see it all. You know I called it a cosmopolitan rats nest containing much rubbish & common place stuff as well as things novel & precious. Well, now that I have seen it, it seems just such a rats nest still, & what do you think was one of the first things I saw when I entered the nearest of the huge buildings. A huge rats nest in a glass case about 8 feet square, with stuffed wood rats looking out from the mass of sticks & leaves etc. natural as life. So you see as usual I am [always?] right! I most enjoyed the art galleries. There are about eighteen acres of paintings by every nation under the sun & I wandered & gazed until I was ready to fall down with utter exhaustion. The art gallery of the California building is quite small & of little significance, not more than a dozen or two of paintings all told – 4 by Keith, not his best, & 4 by Hill not his best, & a few others of no special character by others except a good small one by Yelland. But the national galleries are perfectly overwhelming in grandeur & bulk & variety... The outside view of the buildings is grand & also beautiful. For the best architects have done their best in building them while Frederick Law Olmsted laid out the grounds. Last night the buildings & terraces & fountains along the canals were illuminated by tens of thousands of electric lights arranged along miles of lines of gables, domes & cornices with glorious effect. it was all fairyland on a scale & would have made the Queen of Sheba & poor Solomon in all their glory feel sick with helpless envy." Letter from John Muir to Louie [Strentzel Muir, 1893 May 29.
Early in July 1896, Muir joined the Forestry Commission in Chicago, and with Sargent, Brewer, Hague, and Abbot proceeded to South Dakota to inspect the Black Hills forests of yellow pine . Muir, looking upon the hills denuded by mining operations, fires, and illegal cutting, wrote home : "Wherever the white man goes, the groves vanish ." He continued on with the Forestry Commission to Yellowstone, Idaho, Oregon and Washington. After an interlude in August, Muir returned to the Forestry Commission at Crater Lake. He tours with them the southern Cascades, Santa Lucia coast range, Grand Canyon, and South Sierra.